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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttctagacacactgcgctcctgttcagaacaacgtagacacttctttttttaaactcgtgtgattgtccag

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 18
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71433813|gb|DR814863.1|DR814863
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|61119124|gb|DN560085.1|DN560085
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|149028360|gb|EE154632.2|EE154632
EST:     GAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: GAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|211174833|gb|FL413958.1|FL413958
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|76924990|gb|DV170231.1|DV170231
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|8930105|gb|BE224943.1|BE224943
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|149003161|gb|EE038899.2|EE038899
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|60337715|gb|DN204688.1|DN204688
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|47961688|gb|CN844397.1|CN844397
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|211274102|gb|FL440043.1|FL440043
EST:     AGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: AGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|148945040|gb|EC890224.2|EC890224
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|50331518|gb|CO526644.1|CO526644
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATTTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|50331481|gb|CO526607.1|CO526607
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|91053971|gb|EB164389.1|EB164389
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
EST: gi|88758153|gb|DY542294.1|DY542294
EST:     CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG                         GAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG
genomic: CGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 148

TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 181

TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 161

TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 169

TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttc ... gattgtccagGAACCGAGAAGGCTGCTGCAGTTACAAAGATGAGCCTGACACTATCTGCTGACCATCGTGTATTTGATGGGCAAGTAGGAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATGgtatattttctagacacactgcgctcctgttcagaacaacgtagacacttctttttttaaactcgtgtgattgtccag

- - - - - - - - - -  AGAGGA